def tearDown(self):
""" Close temporary DICOM database and remove temporary data
"""
import shutil
if self.originalDicomDatabase:
DICOMUtils.closeTemporaryDatabase(self.originalDicomDatabase, True)
shutil.rmtree(self.tempDicomDatabase) # closeTemporaryDatabase cleanup doesn't work. We need to do it manually
self.originalDicomDatabase = None
class JRC2013VisTest(unittest.TestCase):
"""
This is the test case for your scripted module.
"""
def delayDisplay(self, message, msec=1000):
"""This utility method displays a small dialog and waits.
This does two things: 1) it lets the event loop catch up
to the state of the test so that rendering and widget updates
have all taken place before the test continues and 2) it
shows the user/developer/tester the state of the test
so that we'll know when it breaks.
"""
print(message)
self.info = qt.QDialog()
self.infoLayout = qt.QVBoxLayout()
self.info.setLayout(self.infoLayout)
self.label = qt.QLabel(message, self.info)
self.infoLayout.addWidget(self.label)
qt.QTimer.singleShot(msec, self.info.close)
self.info.exec_()
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
self.delayDisplay("Closing the scene")
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
slicer.mrmlScene.Clear(0)
def clickAndDrag(self,
widget,
button='Left',
start=(10, 10),
end=(10, 40),
steps=20,
modifiers=[]):
"""Send synthetic mouse events to the specified widget (qMRMLSliceWidget or qMRMLThreeDView)
button : "Left", "Middle", "Right", or "None"
start, end : window coordinates for action
steps : number of steps to move in
modifiers : list containing zero or more of "Shift" or "Control"
"""
style = widget.interactorStyle()
interator = style.GetInteractor()
if button == 'Left':
down = style.OnLeftButtonDown
up = style.OnLeftButtonUp
elif button == 'Right':
down = style.OnRightButtonDown
up = style.OnRightButtonUp
elif button == 'Middle':
down = style.OnMiddleButtonDown
up = style.OnMiddleButtonUp
elif button == 'None' or not button:
down = lambda: None
up = lambda: None
else:
raise Exception("Bad button - should be Left or Right, not %s" %
button)
if 'Shift' in modifiers:
interator.SetShiftKey(1)
if 'Control' in modifiers:
interator.SetControlKey(1)
interator.SetEventPosition(*start)
down()
for step in xrange(steps):
frac = float(step) / steps
x = int(start[0] + frac * (end[0] - start[0]))
y = int(start[1] + frac * (end[1] - start[1]))
interator.SetEventPosition(x, y)
style.OnMouseMove()
up()
interator.SetShiftKey(0)
interator.SetControlKey(0)
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_Part1DICOM()
self.setUp()
self.test_Part2Head()
self.setUp()
self.test_Part3Liver()
self.setUp()
self.test_Part4Lung()
def test_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (('http://slicer.kitware.com/midas3/download?items=18822',
'Dcmtk-db.zip'), )
self.delayDisplay("Downloading")
for url, name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' %
(name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise (UserWarning("Could not find dcmqrscp executable"))
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy(
'1.2.124.113932.1.170.223.162.178.20050502.160340.12640015')
popen.kill()
dicomWidget.detailsPopup.open()
# click on the first row of the tree
index = dicomWidget.tree.indexAt(qt.QPoint(0, 0))
dicomWidget.onTreeClicked(index)
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
self.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.delayDisplay('Change Window')
self.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
self.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
self.delayDisplay('Pan')
self.clickAndDrag(redWidget,
button='Middle',
start=(10, 10),
end=(40, 40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
self.clickAndDrag(redWidget,
button='None',
start=(100, 100),
end=(140, 140),
modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView, button='Right')
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
def test_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='Dcmtk-db.zip',
uris=TESTING_DATA_URL + 'MD5/7a43d121a51a631ab0df02071e5ba6ed',
checksums='MD5:7a43d121a51a631ab0df02071e5ba6ed')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
print("configFilePath: " + os.path.abspath(configFilePath))
print("processCurrentPath: " + os.path.abspath(processCurrentPath))
dcmqrscpExeOptions = ('/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
'/../DCMTK-build/bin/Release',
'/../DCMTK-build/bin/Debug',
'/../DCMTK-build/bin/RelWithDebInfo'
'/../DCMTK-build/bin/MinSizeRel')
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise UserWarning("Could not find dcmqrscp executable")
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
slicer.util.selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy(
'1.2.124.113932.1.170.223.162.178.20050502.160340.12640015')
popen.kill()
# Select first patient
browserWidget = slicer.modules.DICOMWidget.browserWidget
browserWidget.dicomBrowser.dicomTableManager().patientsTable(
).selectFirst()
browserWidget.examineForLoading()
self.delayDisplay('Loading Selection')
browserWidget.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.delayDisplay('Change Window')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
slicer.util.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
self.delayDisplay('Pan')
slicer.util.clickAndDrag(redWidget,
button='Middle',
start=(10, 10),
end=(40, 40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
slicer.util.clickAndDrag(redWidget,
button='None',
start=(100, 100),
end=(140, 140),
modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView, button='Right')
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
class JRC2013VisTestTest(ScriptedLoadableModuleTest):
"""
This is the test case for your scripted module.
"""
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
self.delayDisplay("Closing the scene")
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
slicer.mrmlScene.Clear(0)
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_Part1DICOM()
self.setUp()
self.test_Part2Head()
self.setUp()
self.test_Part3Liver()
self.setUp()
self.test_Part4Lung()
def test_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
SampleData.downloadFromURL(
fileNames='Dcmtk-db.zip',
uris='http://slicer.kitware.com/midas3/download?items=18822')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise (UserWarning("Could not find dcmqrscp executable"))
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy(
'1.2.124.113932.1.170.223.162.178.20050502.160340.12640015')
popen.kill()
dicomWidget.detailsPopup.open()
# click on the first row of the tree
index = dicomWidget.tree.indexAt(qt.QPoint(0, 0))
dicomWidget.onTreeClicked(index)
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.delayDisplay('Change Window')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
slicer.util.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
self.delayDisplay('Pan')
slicer.util.clickAndDrag(redWidget,
button='Middle',
start=(10, 10),
end=(40, 40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
slicer.util.clickAndDrag(redWidget,
button='None',
start=(100, 100),
end=(140, 140),
modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView, button='Right')
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
def test_AlternateReaders(self):
""" Test the DICOM loading of sample testing data
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
referenceData = [
{ "url": "http://slicer.kitware.com/midas3/download?items=292839",
"checksum": "SHA256:3450ef9372a3460a2f181c8d3bb35a74b4f0acb10c6e18cfcf7804e1d99bf843",
"fileName": "Mouse-MR-example-where-GDCM_fails.zip",
"name": "Mouse-MR-example-where-GDCM_fails",
"seriesUID": "1.3.6.1.4.1.9590.100.1.2.366426457713813178933224342280246227461",
# GDCM rejects loading.
# DCMTK reads it but then ITK rejects loading the image with 0 spacing.
"expectedFailures": ["GDCM", "Archetype", "DCMTK", "GDCM with DCMTK fallback"],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
},
{ "url": "http://slicer.kitware.com/midas3/download?items=294857",
"checksum": "SHA256:899f3f8617ca53bad7dca0b2908478319e708b48ff41dfa64b6bac1d76529928",
"fileName": "deidentifiedMRHead-dcm-one-series.zip",
"name": "deidentifiedMRHead-dcm-one-series",
"seriesUID": "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0",
"expectedFailures": [],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
}
]
# another dataset that could be added in the future - currently fails for all readers
# due to invalid format - see https://issues.slicer.org/view.php?id=3569
#{ "url": "http://slicer.kitware.com/midas3/download/item/293587/RIDER_bug.zip",
#"fileName": "RIDER_bug.zip",
#"name": "RIDER_bug",
#"seriesUID": "1.3.6.1.4.1.9328.50.7.261772317324041365541450388603508531852",
#"expectedFailures": []
#}
loadingResult = {}
#
# first, get the data - a zip file of dicom data
#
self.delayDisplay("Downloading")
for dataset in referenceData:
try:
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames=dataset['fileName'], uris=dataset['url'], checksums=dataset['checksum'])[0]
self.delayDisplay('Finished with download')
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
slicer.util.selectModule("DICOM")
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory, dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
#
# select the series
#
browserWidget.onSeriesSelected([dataset['seriesUID']])
# load the data by series UID
browserWidget.examineForLoading()
loadable = list(browserWidget.getAllSelectedLoadables().keys())[0]
#
# try loading using each of the selected readers, fail
# on enexpected load issue
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
readerApproaches = scalarVolumePlugin.readerApproaches()
basename = loadable.name
volumesByApproach = {}
for readerApproach in readerApproaches:
self.delayDisplay('Loading Selection with approach: %s' % readerApproach)
loadable.name = basename + "-" + readerApproach
volumeNode = scalarVolumePlugin.load(loadable,readerApproach)
if not volumeNode and readerApproach not in dataset['expectedFailures']:
raise Exception("Expected to be able to read with %s, but couldn't" % readerApproach)
if volumeNode and readerApproach in dataset['expectedFailures']:
raise Exception("Expected to NOT be able to read with %s, but could!" % readerApproach)
if volumeNode:
volumesByApproach[readerApproach] = volumeNode
self.delayDisplay('Test quantity and unit')
if 'voxelValueQuantity' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueQuantity().GetAsPrintableString(), dataset['voxelValueQuantity'])
if 'voxelValueUnits' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueUnits().GetAsPrintableString(), dataset['voxelValueUnits'])
#
# for each approach that loaded as expected, compare the volumes
# to ensure they match in terms of pixel data and metadata
#
failedComparisons = {}
approachesThatLoaded = list(volumesByApproach.keys())
print('approachesThatLoaded %s' % approachesThatLoaded)
for approachIndex in range(len(approachesThatLoaded)):
firstApproach = approachesThatLoaded[approachIndex]
firstVolume = volumesByApproach[firstApproach]
for secondApproachIndex in range(approachIndex+1,len(approachesThatLoaded)):
secondApproach = approachesThatLoaded[secondApproachIndex]
secondVolume = volumesByApproach[secondApproach]
print('comparing %s,%s' % (firstApproach, secondApproach))
comparison = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin'].compareVolumeNodes(firstVolume,secondVolume)
if comparison != "":
print(('failed: %s', comparison))
failedComparisons[firstApproach,secondApproach] = comparison
if len(failedComparisons.keys()) > 0:
raise Exception("Loaded volumes don't match: %s" % failedComparisons)
self.delayDisplay('%s Test passed!' % dataset['name'])
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('%s Test caused exception!\n' % dataset['name'] + str(e))
testPass = False
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
slicer.util.selectModule('DICOMReaders')
logging.info(loadingResult)
return testPass
def test_MissingSlices(self):
""" Test behavior of the readers when slices are missing
To edit and run this test from the python console, paste this below:
reloadScriptedModule('DICOMReaders'); import DICOMReaders; tester = DICOMReaders.DICOMReadersTest(); tester.setUp(); tester.test_MissingSlices()
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
settings = qt.QSettings()
settings.setValue("DICOM/ScalarVolume/AcquisitionGeometryRegularization", "transform")
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='deidentifiedMRHead-dcm-one-series.zip',
uris='http://slicer.kitware.com/midas3/download?items=294857',
checksums='SHA256:899f3f8617ca53bad7dca0b2908478319e708b48ff41dfa64b6bac1d76529928')[0]
self.delayDisplay('Finished with download\n')
seriesUID = "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0"
seriesRASBounds = [-87.29489517211913, 81.70450973510744,
-121.57139587402344, 134.42860412597656,
-138.71430206298828, 117.28569793701172]
seriesDirectory = "Series 004 [MR - SAG RF FAST VOL FLIP 20]"
lastSliceCorners = [[[81.05451202, 133.92860413, 116.78569794], [81.05451202, -122.07139587, 116.78569794]],
[[81.05451202, 133.92860413, -139.21429443], [81.05451202, -122.07139587, -139.21429443]]]
filesToRemove = [
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.361.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.362.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.363.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.364.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.365.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.366.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.367.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.368.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.369.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.370.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.371.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.372.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.373.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.374.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.375.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.376.0.dcm",
]
try:
print('Removing %d files from the middle of the series' % len(filesToRemove))
for file in filesToRemove:
filePath = os.path.join(dicomFilesDirectory, seriesDirectory, file)
os.remove(filePath)
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
slicer.util.selectModule("DICOM")
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory, dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
#
# select the series
#
browserWidget.onSeriesSelected([seriesUID])
# load the data by series UID
browserWidget.examineForLoading()
loadable = list(browserWidget.getAllSelectedLoadables().keys())[0]
if len(loadable.warning) == 0:
raise Exception("Expected warning about geometry issues due to missing slices!")
#
# load and correct for acquisition then check the geometry
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
volumeNode = scalarVolumePlugin.load(loadable)
if not numpy.allclose(scalarVolumePlugin.acquisitionModeling.fixedCorners[-1], lastSliceCorners):
raise Exception("Acquisition transform didn't fix slice corners!")
self.delayDisplay('test_MissingSlices passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Missing Slices Test caused exception!\n' + str(e))
testPass = False
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
slicer.util.selectModule('DICOMReaders')
return testPass
def test_Part1DICOM(self,enableScreenshotsFlag=0,screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
logic = RSNAVisTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='dataset1_Thorax_Abdomen.zip',
uris='http://slicer.kitware.com/midas3/download?items=124183')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget = slicer.modules.DICOMWidget
dicomWidget.detailsPopup.open()
# load the data by series UID
dicomWidget.detailsPopup.offerLoadables('1.3.12.2.1107.5.1.4.50025.30000005060811542834300000776','Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
logic.takeScreenshot('LoadingADICOMVolume-Loaded','Loaded DICOM Volume',-1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
logic.takeScreenshot('LoadingADICOMVolume-WL','Changed level and window',-1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
logic.takeScreenshot('LoadingADICOMVolume-LinkView','Linked and visible',-1)
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
logic.takeScreenshot('LoadingADICOMVolume-Zoom','Zoom',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('LoadingADICOMVolume-Rotate','Rotate',-1)
threeDView.resetFocalPoint()
logic.takeScreenshot('LoadingADICOMVolume-Center','Center the view',-1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView)
logic.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen','Conventional Widescreen Layout',-1)
slicer.util.mainWindow().moduleSelector().selectModule('VolumeRendering')
logic.takeScreenshot('VolumeRendering-Module','Volume Rendering',-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation()
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName('6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
logic.takeScreenshot('VolumeRendering-SelectVolume','Select the volume 6: CT_Thorax_Abdomen',-1)
presetsScene = slicer.modules.volumerendering.logic().GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.applyPreset(ctCardiac3)
logic.takeScreenshot('VolumeRendering-SelectPreset','Select the Preset CT-Cardiac-3')
self.delayDisplay('Skipping: Select VTK CPU Ray Casting')
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName('VolumeRendering')
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ViewRendering','View Volume Rendering',-1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False);
logic.takeScreenshot('VolumeRendering-SlicesOff','Turn off visibility of slices in 3D',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('VolumeRendering-RotateVolumeRendering','Rotate volume rendered image',-1)
volumeRenderingNode.SetVisibility(0)
logic.takeScreenshot('VolumeRendering-TurnOffVolumeRendering','Turn off volume rendered image',-1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName('AnnotationROI')
annotationROI.SetDisplayVisibility(1)
logic.takeScreenshot('VolumeRendering-DisplayROI','Enable cropping and display ROI',-1)
redWidget.sliceController().setSliceVisible(True)
logic.takeScreenshot('VolumeRendering-SlicesOn','Turn on visibility of slices in 3D',-1)
annotationROI.SetXYZ(-79.61,154.16,-232.591)
annotationROI.SetRadiusXYZ(43.4,65.19,70.5)
logic.takeScreenshot('VolumeRendering-SizedROI','Position the ROI over a kidney',-1)
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ROIRendering','ROI volume rendered',-1)
annotationROI.SetXYZ(15,146,-186)
annotationROI.SetRadiusXYZ(138,57,61)
logic.takeScreenshot('VolumeRendering-BothKidneys','Rendered both kidneys',-1)
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
class RSNAVisTutorialTest(unittest.TestCase):
"""
This is the test case for your scripted module.
"""
def delayDisplay(self,message,msec=1000):
"""This utility method displays a small dialog and waits.
This does two things: 1) it lets the event loop catch up
to the state of the test so that rendering and widget updates
have all taken place before the test continues and 2) it
shows the user/developer/tester the state of the test
so that we'll know when it breaks.
"""
print(message)
self.info = qt.QDialog()
self.infoLayout = qt.QVBoxLayout()
self.info.setLayout(self.infoLayout)
self.label = qt.QLabel(message,self.info)
self.infoLayout.addWidget(self.label)
qt.QTimer.singleShot(msec, self.info.close)
self.info.exec_()
def takeScreenshot(self,name,description,type=-1):
# show the message even if not taking a screen shot
self.delayDisplay(description)
if self.enableScreenshots == 0:
return
lm = slicer.app.layoutManager()
# switch on the type to get the requested window
widget = 0
if type == slicer.qMRMLScreenShotDialog.FullLayout:
# full layout
widget = lm.viewport()
elif type == slicer.qMRMLScreenShotDialog.ThreeD:
# just the 3D window
widget = lm.threeDWidget(0).threeDView()
elif type == slicer.qMRMLScreenShotDialog.Red:
# red slice window
widget = lm.sliceWidget("Red")
elif type == slicer.qMRMLScreenShotDialog.Yellow:
# yellow slice window
widget = lm.sliceWidget("Yellow")
elif type == slicer.qMRMLScreenShotDialog.Green:
# green slice window
widget = lm.sliceWidget("Green")
else:
# default to using the full window
widget = slicer.util.mainWindow()
# reset the type so that the node is set correctly
type = slicer.qMRMLScreenShotDialog.FullLayout
# grab and convert to vtk image data
qpixMap = qt.QPixmap().grabWidget(widget)
qimage = qpixMap.toImage()
imageData = vtk.vtkImageData()
slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)
annotationLogic = slicer.modules.annotations.logic()
annotationLogic.CreateSnapShot(name, description, type, self.screenshotScaleFactor, imageData)
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
self.delayDisplay("Closing the scene")
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
slicer.mrmlScene.Clear(0)
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_Part1DICOM()
self.setUp()
self.test_Part2Head()
self.setUp()
self.test_Part3Liver()
self.setUp()
self.test_Part4Lung()
def test_Part1DICOM(self,enableScreenshotsFlag=0,screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
self.enableScreenshots = enableScreenshotsFlag
self.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=124183', 'dataset1_Thorax_Abdomen.zip'),
)
self.delayDisplay("Downloading")
for url,name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget = slicer.modules.DICOMWidget
dicomWidget.detailsPopup.open()
# load the data by series UID
dicomWidget.detailsPopup.offerLoadables('1.3.12.2.1107.5.1.4.50025.30000005060811542834300000776','Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.takeScreenshot('LoadingADICOMVolume-Loaded','Loaded DICOM Volume',-1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
self.takeScreenshot('LoadingADICOMVolume-WL','Changed level and window',-1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
self.takeScreenshot('LoadingADICOMVolume-LinkView','Linked and visible',-1)
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.takeScreenshot('LoadingADICOMVolume-Zoom','Zoom',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
self.takeScreenshot('LoadingADICOMVolume-Rotate','Rotate',-1)
threeDView.resetFocalPoint()
self.takeScreenshot('LoadingADICOMVolume-Center','Center the view',-1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView)
self.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen','Conventional Widescreen Layout',-1)
slicer.util.mainWindow().moduleSelector().selectModule('VolumeRendering')
self.takeScreenshot('VolumeRendering-Module','Volume Rendering',-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation()
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName('6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
self.takeScreenshot('VolumeRendering-SelectVolume','Select the volume 6: CT_Thorax_Abdomen',-1)
presetsScene = slicer.modules.volumerendering.logic().GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.applyPreset(ctCardiac3)
self.takeScreenshot('VolumeRendering-SelectPreset','Select the Preset CT-Cardiac-3')
self.delayDisplay('Skipping: Select VTK CPU Ray Casting')
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName('VolumeRendering')
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot('VolumeRendering-ViewRendering','View Volume Rendering',-1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False);
self.takeScreenshot('VolumeRendering-SlicesOff','Turn off visibility of slices in 3D',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
self.takeScreenshot('VolumeRendering-RotateVolumeRendering','Rotate volume rendered image',-1)
volumeRenderingNode.SetVisibility(0)
self.takeScreenshot('VolumeRendering-TurnOffVolumeRendering','Turn off volume rendered image',-1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName('AnnotationROI')
annotationROI.SetDisplayVisibility(1)
self.takeScreenshot('VolumeRendering-DisplayROI','Enable cropping and display ROI',-1)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot('VolumeRendering-SlicesOn','Turn on visibility of slices in 3D',-1)
annotationROI.SetXYZ(-79.61,154.16,-232.591)
annotationROI.SetRadiusXYZ(43.4,65.19,70.5)
self.takeScreenshot('VolumeRendering-SizedROI','Position the ROI over a kidney',-1)
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot('VolumeRendering-ROIRendering','ROI volume rendered',-1)
annotationROI.SetXYZ(15,146,-186)
annotationROI.SetRadiusXYZ(138,57,61)
self.takeScreenshot('VolumeRendering-BothKidneys','Rendered both kidneys',-1)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
class RSNAVisTutorialTest(ScriptedLoadableModuleTest):
"""
This is the test case for your scripted module.
Uses ScriptedLoadableModuleTest base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def setUp(self):
""" Do whatever is needed to reset the state - typically a scene clear will be enough.
"""
self.delayDisplay("Closing the scene")
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
slicer.mrmlScene.Clear(0)
def runTest(self):
"""Run as few or as many tests as needed here.
"""
self.setUp()
self.test_Part1DICOM()
self.setUp()
self.test_Part2Head()
self.setUp()
self.test_Part3Liver()
self.setUp()
self.test_Part4Lung()
def test_Part1DICOM(self,enableScreenshotsFlag=0,screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
logic = RSNAVisTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='dataset1_Thorax_Abdomen.zip',
uris='http://slicer.kitware.com/midas3/download?items=124183')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget = slicer.modules.DICOMWidget
dicomWidget.detailsPopup.open()
# load the data by series UID
dicomWidget.detailsPopup.offerLoadables('1.3.12.2.1107.5.1.4.50025.30000005060811542834300000776','Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
logic.takeScreenshot('LoadingADICOMVolume-Loaded','Loaded DICOM Volume',-1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
logic.takeScreenshot('LoadingADICOMVolume-WL','Changed level and window',-1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
logic.takeScreenshot('LoadingADICOMVolume-LinkView','Linked and visible',-1)
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
logic.takeScreenshot('LoadingADICOMVolume-Zoom','Zoom',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('LoadingADICOMVolume-Rotate','Rotate',-1)
threeDView.resetFocalPoint()
logic.takeScreenshot('LoadingADICOMVolume-Center','Center the view',-1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView)
logic.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen','Conventional Widescreen Layout',-1)
slicer.util.mainWindow().moduleSelector().selectModule('VolumeRendering')
logic.takeScreenshot('VolumeRendering-Module','Volume Rendering',-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation()
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName('6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
logic.takeScreenshot('VolumeRendering-SelectVolume','Select the volume 6: CT_Thorax_Abdomen',-1)
presetsScene = slicer.modules.volumerendering.logic().GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.applyPreset(ctCardiac3)
logic.takeScreenshot('VolumeRendering-SelectPreset','Select the Preset CT-Cardiac-3')
self.delayDisplay('Skipping: Select VTK CPU Ray Casting')
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName('VolumeRendering')
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ViewRendering','View Volume Rendering',-1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False);
logic.takeScreenshot('VolumeRendering-SlicesOff','Turn off visibility of slices in 3D',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('VolumeRendering-RotateVolumeRendering','Rotate volume rendered image',-1)
volumeRenderingNode.SetVisibility(0)
logic.takeScreenshot('VolumeRendering-TurnOffVolumeRendering','Turn off volume rendered image',-1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName('AnnotationROI')
annotationROI.SetDisplayVisibility(1)
logic.takeScreenshot('VolumeRendering-DisplayROI','Enable cropping and display ROI',-1)
redWidget.sliceController().setSliceVisible(True)
logic.takeScreenshot('VolumeRendering-SlicesOn','Turn on visibility of slices in 3D',-1)
annotationROI.SetXYZ(-79.61,154.16,-232.591)
annotationROI.SetRadiusXYZ(43.4,65.19,70.5)
logic.takeScreenshot('VolumeRendering-SizedROI','Position the ROI over a kidney',-1)
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ROIRendering','ROI volume rendered',-1)
annotationROI.SetXYZ(15,146,-186)
annotationROI.SetRadiusXYZ(138,57,61)
logic.takeScreenshot('VolumeRendering-BothKidneys','Rendered both kidneys',-1)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
def test_Part1DICOM(self,
enableScreenshotsFlag=0,
screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
logic = RSNAVisTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='dataset1_Thorax_Abdomen.zip',
uris=TESTING_DATA_URL +
'SHA256/17a4199aad03a373dab27dc17e5bfcf84fc194d0a30975b4073e5b595d43a56a',
checksums=
'SHA256:17a4199aad03a373dab27dc17e5bfcf84fc194d0a30975b4073e5b595d43a56a'
)[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatabase')
slicer.util.selectModule('DICOM')
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory,
dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
# load the data by series UID
dicomBrowser.dicomTableManager().patientsTable().selectFirst()
browserWidget.examineForLoading()
self.delayDisplay('Loading Selection')
browserWidget.loadCheckedLoadables()
logic.takeScreenshot('LoadingADICOMVolume-Loaded',
'Loaded DICOM Volume', -1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
logic.takeScreenshot('LoadingADICOMVolume-WL',
'Changed level and window', -1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
logic.takeScreenshot('LoadingADICOMVolume-LinkView',
'Linked and visible', -1)
slicer.util.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
logic.takeScreenshot('LoadingADICOMVolume-Zoom', 'Zoom', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('LoadingADICOMVolume-Rotate', 'Rotate', -1)
threeDView.resetFocalPoint()
logic.takeScreenshot('LoadingADICOMVolume-Center',
'Center the view', -1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.
SlicerLayoutConventionalWidescreenView)
logic.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen',
'Conventional Widescreen Layout', -1)
slicer.util.mainWindow().moduleSelector().selectModule(
'VolumeRendering')
logic.takeScreenshot('VolumeRendering-Module', 'Volume Rendering',
-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation(
)
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName(
'6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
logic.takeScreenshot('VolumeRendering-SelectVolume',
'Select the volume 6: CT_Thorax_Abdomen', -1)
presetsScene = slicer.modules.volumerendering.logic(
).GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.mrmlVolumePropertyNode().Copy(ctCardiac3)
logic.takeScreenshot('VolumeRendering-SelectPreset',
'Select the Preset CT-Cardiac-3')
self.delayDisplay('Skipping: Select VTK CPU Ray Casting')
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName(
'VolumeRendering')
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ViewRendering',
'View Volume Rendering', -1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False)
logic.takeScreenshot('VolumeRendering-SlicesOff',
'Turn off visibility of slices in 3D', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('VolumeRendering-RotateVolumeRendering',
'Rotate volume rendered image', -1)
volumeRenderingNode.SetVisibility(0)
logic.takeScreenshot('VolumeRendering-TurnOffVolumeRendering',
'Turn off volume rendered image', -1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName(
'AnnotationROI')
annotationROI.SetDisplayVisibility(1)
logic.takeScreenshot('VolumeRendering-DisplayROI',
'Enable cropping and display ROI', -1)
redWidget.sliceController().setSliceVisible(True)
logic.takeScreenshot('VolumeRendering-SlicesOn',
'Turn on visibility of slices in 3D', -1)
annotationROI.SetXYZ(-79.61, 154.16, -232.591)
annotationROI.SetRadiusXYZ(43.4, 65.19, 70.5)
logic.takeScreenshot('VolumeRendering-SizedROI',
'Position the ROI over a kidney', -1)
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ROIRendering',
'ROI volume rendered', -1)
annotationROI.SetXYZ(15, 146, -186)
annotationROI.SetRadiusXYZ(138, 57, 61)
logic.takeScreenshot('VolumeRendering-BothKidneys',
'Rendered both kidneys', -1)
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
def test_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
SampleData.downloadFromURL(
fileNames='Dcmtk-db.zip',
uris='http://slicer.kitware.com/midas3/download?items=18822')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise UserWarning("Could not find dcmqrscp executable")
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args, stdout=subprocess.PIPE, cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy('1.2.124.113932.1.170.223.162.178.20050502.160340.12640015');
popen.kill()
dicomWidget.detailsPopup.open()
# click on the first row of the tree
index = dicomWidget.tree.indexAt(qt.QPoint(0,0))
dicomWidget.onTreeClicked(index)
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
self.delayDisplay('Change Window')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.delayDisplay('Pan')
slicer.util.clickAndDrag(redWidget,button='Middle',start=(10,10),end=(40,40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
slicer.util.clickAndDrag(redWidget,button='None',start=(100,100),end=(140,140),modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView,button='Right')
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
